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Manganese in PDB 5ws6: Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset

Enzymatic activity of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset

All present enzymatic activity of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset:
1.10.3.9;

Protein crystallography data

The structure of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset, PDB code: 5ws6 was solved by M.Suga, J.R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.960, 230.220, 286.020, 90.00, 90.00, 90.00
R / Rfree (%) 12.9 / 17.5

Other elements in 5ws6:

The structure of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset also contains other interesting chemical elements:

Magnesium (Mg) 72 atoms
Iron (Fe) 8 atoms
Calcium (Ca) 12 atoms
Chlorine (Cl) 4 atoms

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Manganese atom in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset (pdb code 5ws6). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 16 binding sites of Manganese where determined in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset, PDB code: 5ws6:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 16 in 5ws6

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Manganese binding site 1 out of 16 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn414

b:49.0
occ:0.20
 MN1 A:OEX414 0.0 49.0 0.2
MN1 A:OEY415 0.2 49.4 0.8
OE2 A:GLU189 1.8 49.8 0.2
OE2 A:GLU189 1.8 50.0 0.8
O1 A:OEX414 1.8 47.7 0.2
O3 A:OEX414 1.9 46.3 0.2
O3 A:OEY415 2.0 46.6 0.8
O1 A:OEY415 2.0 48.5 0.8
NE2 A:HIS332 2.0 45.6 0.8
NE2 A:HIS332 2.1 44.7 0.2
O6 A:OEY415 2.2 56.7 0.4
OD2 A:ASP342 2.2 43.7 0.8
OD2 A:ASP342 2.2 44.2 0.2
MN2 A:OEX414 2.6 49.6 0.2
O5 A:OEX414 2.7 59.1 0.2
O5 A:OEY415 2.7 55.7 0.8
MN2 A:OEY415 2.8 49.8 0.8
CD A:GLU189 2.9 49.0 0.2
CD A:GLU189 2.9 47.6 0.8
CD2 A:HIS332 2.9 42.5 0.8
CE1 A:HIS332 3.0 46.2 0.2
CE1 A:HIS332 3.0 46.5 0.8
CG A:ASP342 3.1 44.0 0.2
CG A:ASP342 3.1 45.4 0.8
CD2 A:HIS332 3.1 43.3 0.2
MN3 A:OEX414 3.2 44.9 0.2
MN3 A:OEY415 3.2 49.6 0.8
OD1 A:ASP342 3.3 44.5 0.2
OD1 A:ASP342 3.4 43.5 0.8
OE1 A:GLU189 3.4 49.7 0.8
OE1 A:GLU189 3.5 49.1 0.2
O2 A:OEX414 3.5 45.1 0.2
CA1 A:OEY415 3.5 46.9 0.8
O2 A:OEY415 3.5 43.9 0.8
CA1 A:OEX414 3.6 50.5 0.2
OE1 A:GLU333 3.8 48.5 0.8
NE2 A:HIS337 3.9 44.7 0.8
OE1 A:GLU333 3.9 48.9 0.2
NE2 A:HIS337 3.9 43.6 0.2
CG A:GLU189 4.1 45.6 0.2
CG A:HIS332 4.1 48.6 0.8
ND1 A:HIS332 4.1 46.6 0.2
ND1 A:HIS332 4.1 45.4 0.8
CG A:GLU189 4.1 44.2 0.8
OXT A:ALA344 4.2 48.4 0.2
CG A:HIS332 4.2 45.0 0.2
O A:HOH586 4.3 62.9 1.0
CE1 A:HIS337 4.3 43.0 0.8
OXT A:ALA344 4.3 48.7 0.8
OE1 C:GLU354 4.4 54.9 0.2
OE1 C:GLU354 4.5 57.4 0.8
CB A:ASP342 4.5 42.6 0.2
CB A:ASP342 4.5 43.6 0.8
CE1 A:HIS337 4.5 42.6 0.2
CG1 A:VAL185 4.5 40.7 0.2
OE2 C:GLU354 4.6 54.3 0.8
CD A:GLU333 4.6 49.5 0.8
CG1 A:VAL185 4.6 40.8 0.8
OE2 C:GLU354 4.6 53.2 0.2
O A:ALA344 4.6 46.3 0.2
O A:ALA344 4.7 46.1 0.8
CD A:GLU333 4.7 48.4 0.2
C A:ALA344 4.7 47.4 0.2
O A:HOH620 4.8 48.5 0.8
C A:ALA344 4.8 46.9 0.8
CD C:GLU354 4.9 52.1 0.8
CD C:GLU354 4.9 53.6 0.2
O4 A:OEX414 4.9 48.1 0.2
MN4 A:OEY415 4.9 54.0 0.8
O A:HOH620 5.0 49.5 0.2
MN4 A:OEX414 5.0 55.4 0.2

Manganese binding site 2 out of 16 in 5ws6

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Manganese binding site 2 out of 16 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn414

b:49.6
occ:0.20
 MN2 A:OEX414 0.0 49.6 0.2
MN2 A:OEY415 0.2 49.8 0.8
O1 A:OEY415 1.7 48.5 0.8
O3 A:OEY415 1.8 46.6 0.8
O1 A:OEX414 1.8 47.7 0.2
O2 A:OEY415 1.9 43.9 0.8
O2 A:OEX414 1.9 45.1 0.2
OXT A:ALA344 1.9 48.4 0.2
O3 A:OEX414 1.9 46.3 0.2
OXT A:ALA344 2.0 48.7 0.8
OE1 C:GLU354 2.0 57.4 0.8
OE1 C:GLU354 2.1 54.9 0.2
OD1 A:ASP342 2.1 43.5 0.8
OD1 A:ASP342 2.2 44.5 0.2
MN1 A:OEY415 2.5 49.4 0.8
MN1 A:OEX414 2.6 49.0 0.2
MN3 A:OEY415 2.7 49.6 0.8
MN3 A:OEX414 2.8 44.9 0.2
C A:ALA344 2.8 47.4 0.2
CD C:GLU354 2.9 52.1 0.8
C A:ALA344 2.9 46.9 0.8
CG A:ASP342 2.9 45.4 0.8
CD C:GLU354 2.9 53.6 0.2
OD2 A:ASP342 3.0 43.7 0.8
CG A:ASP342 3.0 44.0 0.2
OE2 C:GLU354 3.1 54.3 0.8
O A:ALA344 3.1 46.3 0.2
O A:ALA344 3.1 46.1 0.8
OE2 C:GLU354 3.2 53.2 0.2
OD2 A:ASP342 3.2 44.2 0.2
CA1 A:OEY415 3.4 46.9 0.8
CA1 A:OEX414 3.4 50.5 0.2
O5 A:OEY415 3.5 55.7 0.8
NE2 A:HIS337 3.5 44.7 0.8
O5 A:OEX414 3.6 59.1 0.2
NE2 A:HIS337 3.7 43.6 0.2
OE2 A:GLU189 3.9 50.0 0.8
O6 A:OEY415 4.0 56.7 0.4
OE2 A:GLU189 4.0 49.8 0.2
CA A:ALA344 4.1 47.0 0.2
OE1 A:GLU333 4.2 48.5 0.8
O A:HOH615 4.2 54.4 1.0
O4 A:OEY415 4.2 50.7 0.8
O4 A:OEX414 4.2 48.1 0.2
N A:ALA344 4.2 51.1 0.2
CG C:GLU354 4.2 54.9 0.8
CD2 A:HIS337 4.3 45.9 0.8
CD2 A:HIS337 4.3 45.1 0.2
CA A:ALA344 4.3 45.1 0.8
O A:HOH586 4.3 62.9 1.0
NE2 A:HIS332 4.3 45.6 0.8
CG C:GLU354 4.3 53.8 0.2
OE1 A:GLU333 4.3 48.9 0.2
CB A:ASP342 4.4 43.6 0.8
NE2 A:HIS332 4.4 44.7 0.2
N A:ALA344 4.4 53.1 0.8
CB A:ASP342 4.5 42.6 0.2
CE1 A:HIS337 4.6 43.0 0.8
NH2 C:ARG357 4.7 42.9 1.0
OD1 A:ASP170 4.7 47.9 0.8
CD A:GLU189 4.7 47.6 0.8
CB C:GLU354 4.8 50.1 0.8
CB C:GLU354 4.8 50.6 0.2
CD A:GLU189 4.8 49.0 0.2
OE1 A:GLU189 4.8 49.7 0.8
C A:ASP342 4.9 47.2 0.2
CE1 A:HIS337 4.9 42.6 0.2
CA A:ASP342 4.9 43.2 0.8
C A:ASP342 4.9 47.1 0.8
CA A:ASP342 4.9 43.8 0.2
OE1 A:GLU189 4.9 49.1 0.2
NH1 C:ARG357 5.0 41.0 1.0
OD1 A:ASP170 5.0 46.0 0.2
O A:ASP342 5.0 50.5 0.8

Manganese binding site 3 out of 16 in 5ws6

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Manganese binding site 3 out of 16 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn414

b:44.9
occ:0.20
 MN3 A:OEX414 0.0 44.9 0.2
MN3 A:OEY415 0.1 49.6 0.8
O2 A:OEX414 1.8 45.1 0.2
O4 A:OEX414 1.9 48.1 0.2
OE1 A:GLU333 1.9 48.5 0.8
O4 A:OEY415 1.9 50.7 0.8
O2 A:OEY415 2.0 43.9 0.8
O5 A:OEY415 2.0 55.7 0.8
O5 A:OEX414 2.0 59.1 0.2
OE1 A:GLU333 2.0 48.9 0.2
O3 A:OEY415 2.1 46.6 0.8
O3 A:OEX414 2.1 46.3 0.2
OE2 C:GLU354 2.1 54.3 0.8
OE2 C:GLU354 2.1 53.2 0.2
MN4 A:OEY415 2.7 54.0 0.8
CD A:GLU333 2.8 49.5 0.8
MN2 A:OEX414 2.8 49.6 0.2
MN4 A:OEX414 2.8 55.4 0.2
CD A:GLU333 2.9 48.4 0.2
MN2 A:OEY415 2.9 49.8 0.8
OE2 A:GLU333 2.9 48.4 0.8
CD C:GLU354 3.1 53.6 0.2
CD C:GLU354 3.1 52.1 0.8
OE2 A:GLU333 3.1 48.7 0.2
O6 A:OEY415 3.2 56.7 0.4
MN1 A:OEX414 3.2 49.0 0.2
MN1 A:OEY415 3.3 49.4 0.8
OE1 C:GLU354 3.3 54.9 0.2
OE1 C:GLU354 3.3 57.4 0.8
O1 A:OEX414 3.5 47.7 0.2
CA1 A:OEX414 3.5 50.5 0.2
O1 A:OEY415 3.6 48.5 0.8
CA1 A:OEY415 3.6 46.9 0.8
OD2 A:ASP170 4.0 50.1 0.8
NH2 C:ARG357 4.0 42.9 1.0
OD1 A:ASP170 4.0 47.9 0.8
NE2 A:HIS337 4.1 43.6 0.2
NE2 A:HIS337 4.1 44.7 0.8
NE2 A:HIS332 4.1 44.7 0.2
O A:HOH536 4.1 54.5 0.8
O C:HOH645 4.2 31.7 0.2
OD2 A:ASP170 4.2 47.2 0.2
CG A:GLU333 4.2 48.1 0.8
OD1 A:ASP170 4.2 46.0 0.2
NE2 A:HIS332 4.2 45.6 0.8
OXT A:ALA344 4.3 48.4 0.2
O A:HOH536 4.3 54.0 0.2
CG A:GLU333 4.3 45.5 0.2
O A:HOH575 4.4 50.9 0.8
CD2 A:HIS332 4.4 43.3 0.2
OXT A:ALA344 4.4 48.7 0.8
CD2 A:HIS332 4.4 42.5 0.8
CG C:GLU354 4.4 54.9 0.8
CG C:GLU354 4.4 53.8 0.2
CG A:ASP170 4.4 43.3 0.8
O A:ALA344 4.5 46.3 0.2
O A:HOH575 4.5 51.4 0.2
O A:HOH525 4.5 49.7 0.8
O A:HOH525 4.6 50.0 0.2
CE1 A:HIS337 4.6 43.0 0.8
O A:ALA344 4.6 46.1 0.8
CG A:ASP170 4.6 45.3 0.2
OE2 A:GLU189 4.7 49.8 0.2
OD1 A:ASP342 4.7 44.5 0.2
CB A:GLU333 4.7 42.2 0.8
OD1 A:ASP342 4.7 43.5 0.8
CB A:GLU333 4.7 43.6 0.2
CE1 A:HIS337 4.8 42.6 0.2
OD2 A:ASP342 4.8 43.7 0.8
OE2 A:GLU189 4.8 50.0 0.8
C A:ALA344 4.9 47.4 0.2
O A:HOH620 4.9 48.5 0.8
OD2 A:ASP342 4.9 44.2 0.2
C A:ALA344 5.0 46.9 0.8

Manganese binding site 4 out of 16 in 5ws6

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Manganese binding site 4 out of 16 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn414

b:55.4
occ:0.20
 MN4 A:OEX414 0.0 55.4 0.2
MN4 A:OEY415 0.2 54.0 0.8
O A:HOH575 1.9 50.9 0.8
OD2 A:ASP170 2.0 50.1 0.8
OE2 A:GLU333 2.0 48.4 0.8
O4 A:OEX414 2.0 48.1 0.2
OD2 A:ASP170 2.0 47.2 0.2
O A:HOH575 2.1 51.4 0.2
OE2 A:GLU333 2.1 48.7 0.2
O4 A:OEY415 2.2 50.7 0.8
O A:HOH525 2.2 50.0 0.2
O A:HOH525 2.3 49.7 0.8
O5 A:OEY415 2.3 55.7 0.8
O5 A:OEX414 2.3 59.1 0.2
MN3 A:OEX414 2.8 44.9 0.2
MN3 A:OEY415 2.9 49.6 0.8
CD A:GLU333 3.0 49.5 0.8
CD A:GLU333 3.1 48.4 0.2
CG A:ASP170 3.1 43.3 0.8
CG A:ASP170 3.1 45.3 0.2
OE1 A:GLU333 3.4 48.9 0.2
OE1 A:GLU333 3.4 48.5 0.8
O6 A:OEY415 3.5 56.7 0.4
OD1 A:ASP170 3.5 47.9 0.8
OD1 A:ASP170 3.5 46.0 0.2
O A:HOH620 3.7 48.5 0.8
O A:HOH620 3.8 49.5 0.2
O A:HOH536 3.8 54.0 0.2
O2 A:OEX414 3.8 45.1 0.2
O A:HOH576 3.8 47.6 1.0
CA1 A:OEX414 3.8 50.5 0.2
O2 A:OEY415 3.9 43.9 0.8
O A:HOH536 4.0 54.5 0.8
OD1 A:ASP61 4.0 44.7 0.8
O A:HOH605 4.0 52.2 1.0
CA1 A:OEY415 4.1 46.9 0.8
O A:SER169 4.1 47.7 0.8
OD1 A:ASP61 4.1 45.0 0.2
CB A:ASP170 4.3 43.2 0.8
O A:SER169 4.3 45.6 0.2
CG A:GLU333 4.3 48.1 0.8
CB A:ASP170 4.4 43.6 0.2
CG A:GLU333 4.4 45.5 0.2
CA A:ASP170 4.4 42.9 0.8
CA A:ASP170 4.5 42.5 0.2
OE2 C:GLU354 4.5 53.2 0.2
OE2 C:GLU354 4.6 54.3 0.8
NH2 C:ARG357 4.6 42.9 1.0
O D:HOH532 4.6 40.5 1.0
O3 A:OEX414 4.7 46.3 0.2
O3 A:OEY415 4.7 46.6 0.8
C A:SER169 4.8 45.9 0.8
C A:SER169 4.8 45.1 0.2
N A:ASP170 4.9 42.7 0.8
O A:HOH540 4.9 50.8 1.0
CG A:ASP61 4.9 44.7 0.8
N A:ASP170 4.9 43.7 0.2
MN1 A:OEX414 5.0 49.0 0.2

Manganese binding site 5 out of 16 in 5ws6

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Manganese binding site 5 out of 16 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn415

b:49.4
occ:0.80
 MN1 A:OEY415 0.0 49.4 0.8
MN1 A:OEX414 0.2 49.0 0.2
O1 A:OEX414 1.7 47.7 0.2
OE2 A:GLU189 1.7 50.0 0.8
OE2 A:GLU189 1.8 49.8 0.2
O1 A:OEY415 1.8 48.5 0.8
O3 A:OEX414 2.0 46.3 0.2
O3 A:OEY415 2.0 46.6 0.8
OD2 A:ASP342 2.1 43.7 0.8
OD2 A:ASP342 2.1 44.2 0.2
NE2 A:HIS332 2.2 45.6 0.8
NE2 A:HIS332 2.3 44.7 0.2
O6 A:OEY415 2.3 56.7 0.4
MN2 A:OEX414 2.5 49.6 0.2
MN2 A:OEY415 2.7 49.8 0.8
O5 A:OEX414 2.8 59.1 0.2
O5 A:OEY415 2.8 55.7 0.8
CD A:GLU189 2.8 47.6 0.8
CD A:GLU189 2.9 49.0 0.2
CG A:ASP342 2.9 44.0 0.2
CG A:ASP342 3.0 45.4 0.8
CE1 A:HIS332 3.1 46.2 0.2
OD1 A:ASP342 3.1 44.5 0.2
CD2 A:HIS332 3.1 42.5 0.8
CE1 A:HIS332 3.1 46.5 0.8
MN3 A:OEX414 3.3 44.9 0.2
MN3 A:OEY415 3.3 49.6 0.8
OD1 A:ASP342 3.3 43.5 0.8
CD2 A:HIS332 3.3 43.3 0.2
OE1 A:GLU189 3.4 49.7 0.8
O2 A:OEX414 3.4 45.1 0.2
OE1 A:GLU189 3.4 49.1 0.2
CA1 A:OEY415 3.4 46.9 0.8
O2 A:OEY415 3.4 43.9 0.8
CA1 A:OEX414 3.5 50.5 0.2
OE1 A:GLU333 3.9 48.5 0.8
NE2 A:HIS337 3.9 44.7 0.8
NE2 A:HIS337 4.0 43.6 0.2
OXT A:ALA344 4.0 48.4 0.2
OE1 A:GLU333 4.0 48.9 0.2
CG A:GLU189 4.0 45.6 0.2
CG A:GLU189 4.1 44.2 0.8
O A:HOH586 4.1 62.9 1.0
OXT A:ALA344 4.2 48.7 0.8
ND1 A:HIS332 4.2 45.4 0.8
ND1 A:HIS332 4.3 46.6 0.2
CG A:HIS332 4.3 48.6 0.8
OE1 C:GLU354 4.3 54.9 0.2
CB A:ASP342 4.4 42.6 0.2
CB A:ASP342 4.4 43.6 0.8
CE1 A:HIS337 4.4 43.0 0.8
OE1 C:GLU354 4.4 57.4 0.8
CG A:HIS332 4.4 45.0 0.2
O A:ALA344 4.5 46.3 0.2
O A:ALA344 4.5 46.1 0.8
C A:ALA344 4.6 47.4 0.2
OE2 C:GLU354 4.6 54.3 0.8
CE1 A:HIS337 4.6 42.6 0.2
OE2 C:GLU354 4.6 53.2 0.2
CG1 A:VAL185 4.7 40.7 0.2
C A:ALA344 4.7 46.9 0.8
CG1 A:VAL185 4.7 40.8 0.8
CD A:GLU333 4.7 49.5 0.8
O A:HOH620 4.8 48.5 0.8
CD C:GLU354 4.8 52.1 0.8
CD A:GLU333 4.8 48.4 0.2
CD C:GLU354 4.9 53.6 0.2
O4 A:OEX414 5.0 48.1 0.2
O A:HOH620 5.0 49.5 0.2

Manganese binding site 6 out of 16 in 5ws6

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Manganese binding site 6 out of 16 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn415

b:49.8
occ:0.80
 MN2 A:OEY415 0.0 49.8 0.8
MN2 A:OEX414 0.2 49.6 0.2
OXT A:ALA344 1.7 48.4 0.2
O1 A:OEY415 1.8 48.5 0.8
OXT A:ALA344 1.8 48.7 0.8
O2 A:OEY415 1.9 43.9 0.8
O1 A:OEX414 1.9 47.7 0.2
O2 A:OEX414 1.9 45.1 0.2
OE1 C:GLU354 2.0 57.4 0.8
O3 A:OEY415 2.0 46.6 0.8
OE1 C:GLU354 2.0 54.9 0.2
OD1 A:ASP342 2.1 43.5 0.8
O3 A:OEX414 2.1 46.3 0.2
OD1 A:ASP342 2.1 44.5 0.2
C A:ALA344 2.7 47.4 0.2
MN1 A:OEY415 2.7 49.4 0.8
C A:ALA344 2.7 46.9 0.8
MN1 A:OEX414 2.8 49.0 0.2
MN3 A:OEY415 2.8 49.6 0.8
CD C:GLU354 2.9 52.1 0.8
MN3 A:OEX414 2.9 44.9 0.2
CG A:ASP342 2.9 45.4 0.8
CD C:GLU354 2.9 53.6 0.2
O A:ALA344 3.0 46.3 0.2
O A:ALA344 3.0 46.1 0.8
CG A:ASP342 3.1 44.0 0.2
OD2 A:ASP342 3.1 43.7 0.8
OE2 C:GLU354 3.2 54.3 0.8
OE2 C:GLU354 3.2 53.2 0.2
OD2 A:ASP342 3.3 44.2 0.2
CA1 A:OEY415 3.4 46.9 0.8
CA1 A:OEX414 3.5 50.5 0.2
NE2 A:HIS337 3.6 44.7 0.8
O5 A:OEY415 3.6 55.7 0.8
O5 A:OEX414 3.7 59.1 0.2
NE2 A:HIS337 3.8 43.6 0.2
CA A:ALA344 4.0 47.0 0.2
OE2 A:GLU189 4.0 50.0 0.8
N A:ALA344 4.1 51.1 0.2
O A:HOH615 4.1 54.4 1.0
CA A:ALA344 4.1 45.1 0.8
O6 A:OEY415 4.1 56.7 0.4
OE2 A:GLU189 4.2 49.8 0.2
CG C:GLU354 4.2 54.9 0.8
O A:HOH586 4.3 62.9 1.0
N A:ALA344 4.3 53.1 0.8
O4 A:OEY415 4.3 50.7 0.8
O4 A:OEX414 4.3 48.1 0.2
CG C:GLU354 4.3 53.8 0.2
CD2 A:HIS337 4.3 45.9 0.8
CD2 A:HIS337 4.3 45.1 0.2
OE1 A:GLU333 4.3 48.5 0.8
CB A:ASP342 4.4 43.6 0.8
CB A:ASP342 4.5 42.6 0.2
NE2 A:HIS332 4.5 45.6 0.8
OE1 A:GLU333 4.5 48.9 0.2
NE2 A:HIS332 4.5 44.7 0.2
NH2 C:ARG357 4.6 42.9 1.0
CB C:GLU354 4.7 50.1 0.8
CE1 A:HIS337 4.7 43.0 0.8
CB C:GLU354 4.7 50.6 0.2
OD1 A:ASP170 4.7 47.9 0.8
C A:ASP342 4.8 47.2 0.2
C A:ASP342 4.8 47.1 0.8
CD A:GLU189 4.8 47.6 0.8
CA A:ASP342 4.8 43.2 0.8
CA A:ASP342 4.8 43.8 0.2
NH1 C:ARG357 4.8 41.0 1.0
OE1 A:GLU189 4.9 49.7 0.8
CD A:GLU189 4.9 49.0 0.2
O A:ASP342 4.9 50.5 0.8
CB A:ALA344 4.9 46.2 0.2
OE1 A:GLU189 5.0 49.1 0.2
O A:ASP342 5.0 49.1 0.2
OD1 A:ASP170 5.0 46.0 0.2
CE1 A:HIS337 5.0 42.6 0.2

Manganese binding site 7 out of 16 in 5ws6

Go back to Manganese Binding Sites List in 5ws6
Manganese binding site 7 out of 16 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn415

b:49.6
occ:0.80
 MN3 A:OEY415 0.0 49.6 0.8
MN3 A:OEX414 0.1 44.9 0.2
O2 A:OEX414 1.7 45.1 0.2
O4 A:OEX414 1.9 48.1 0.2
O2 A:OEY415 1.9 43.9 0.8
O4 A:OEY415 1.9 50.7 0.8
O5 A:OEY415 2.0 55.7 0.8
O5 A:OEX414 2.0 59.1 0.2
OE1 A:GLU333 2.0 48.5 0.8
O3 A:OEY415 2.1 46.6 0.8
OE2 C:GLU354 2.1 54.3 0.8
O3 A:OEX414 2.1 46.3 0.2
OE2 C:GLU354 2.1 53.2 0.2
OE1 A:GLU333 2.2 48.9 0.2
MN2 A:OEX414 2.7 49.6 0.2
MN4 A:OEY415 2.7 54.0 0.8
MN2 A:OEY415 2.8 49.8 0.8
CD A:GLU333 2.9 49.5 0.8
MN4 A:OEX414 2.9 55.4 0.2
CD A:GLU333 3.0 48.4 0.2
CD C:GLU354 3.0 52.1 0.8
CD C:GLU354 3.0 53.6 0.2
OE2 A:GLU333 3.0 48.4 0.8
O6 A:OEY415 3.2 56.7 0.4
OE2 A:GLU333 3.2 48.7 0.2
MN1 A:OEX414 3.2 49.0 0.2
OE1 C:GLU354 3.3 54.9 0.2
MN1 A:OEY415 3.3 49.4 0.8
OE1 C:GLU354 3.3 57.4 0.8
O1 A:OEX414 3.4 47.7 0.2
CA1 A:OEX414 3.5 50.5 0.2
O1 A:OEY415 3.6 48.5 0.8
CA1 A:OEY415 3.6 46.9 0.8
NH2 C:ARG357 3.9 42.9 1.0
OD2 A:ASP170 3.9 50.1 0.8
OD1 A:ASP170 4.0 47.9 0.8
NE2 A:HIS337 4.1 44.7 0.8
NE2 A:HIS337 4.1 43.6 0.2
O A:HOH536 4.1 54.5 0.8
NE2 A:HIS332 4.1 44.7 0.2
OD2 A:ASP170 4.1 47.2 0.2
OD1 A:ASP170 4.2 46.0 0.2
O C:HOH645 4.2 31.7 0.2
OXT A:ALA344 4.2 48.4 0.2
O A:HOH536 4.3 54.0 0.2
NE2 A:HIS332 4.3 45.6 0.8
CG A:GLU333 4.3 48.1 0.8
OXT A:ALA344 4.3 48.7 0.8
CG A:ASP170 4.4 43.3 0.8
CG C:GLU354 4.4 54.9 0.8
CG C:GLU354 4.4 53.8 0.2
O A:HOH575 4.4 50.9 0.8
CG A:GLU333 4.4 45.5 0.2
O A:ALA344 4.4 46.3 0.2
CD2 A:HIS332 4.5 43.3 0.2
CD2 A:HIS332 4.5 42.5 0.8
O A:ALA344 4.5 46.1 0.8
O A:HOH525 4.6 49.7 0.8
O A:HOH575 4.6 51.4 0.2
O A:HOH525 4.6 50.0 0.2
CG A:ASP170 4.6 45.3 0.2
CE1 A:HIS337 4.6 43.0 0.8
OD1 A:ASP342 4.6 44.5 0.2
OD1 A:ASP342 4.7 43.5 0.8
OE2 A:GLU189 4.7 49.8 0.2
C A:ALA344 4.8 47.4 0.2
CB A:GLU333 4.8 42.2 0.8
OD2 A:ASP342 4.8 43.7 0.8
CE1 A:HIS337 4.8 42.6 0.2
OE2 A:GLU189 4.8 50.0 0.8
CB A:GLU333 4.8 43.6 0.2
O A:HOH620 4.8 48.5 0.8
OD2 A:ASP342 4.9 44.2 0.2
C A:ALA344 4.9 46.9 0.8
CZ C:ARG357 5.0 49.5 1.0
O A:HOH620 5.0 49.5 0.2

Manganese binding site 8 out of 16 in 5ws6

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Manganese binding site 8 out of 16 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn415

b:54.0
occ:0.80
 MN4 A:OEY415 0.0 54.0 0.8
MN4 A:OEX414 0.2 55.4 0.2
O4 A:OEX414 1.8 48.1 0.2
OE2 A:GLU333 2.0 48.4 0.8
OD2 A:ASP170 2.0 50.1 0.8
O4 A:OEY415 2.0 50.7 0.8
O A:HOH575 2.1 50.9 0.8
OE2 A:GLU333 2.1 48.7 0.2
OD2 A:ASP170 2.1 47.2 0.2
O A:HOH525 2.2 50.0 0.2
O A:HOH575 2.3 51.4 0.2
O A:HOH525 2.3 49.7 0.8
O5 A:OEY415 2.3 55.7 0.8
O5 A:OEX414 2.3 59.1 0.2
MN3 A:OEX414 2.7 44.9 0.2
MN3 A:OEY415 2.7 49.6 0.8
CD A:GLU333 3.0 49.5 0.8
CD A:GLU333 3.0 48.4 0.2
CG A:ASP170 3.1 43.3 0.8
CG A:ASP170 3.1 45.3 0.2
OE1 A:GLU333 3.3 48.9 0.2
OE1 A:GLU333 3.3 48.5 0.8
OD1 A:ASP170 3.5 47.9 0.8
OD1 A:ASP170 3.5 46.0 0.2
O6 A:OEY415 3.5 56.7 0.4
O A:HOH536 3.6 54.0 0.2
O2 A:OEX414 3.7 45.1 0.2
O2 A:OEY415 3.8 43.9 0.8
O A:HOH620 3.8 48.5 0.8
O A:HOH536 3.8 54.5 0.8
CA1 A:OEX414 3.8 50.5 0.2
O A:HOH620 3.9 49.5 0.2
OD1 A:ASP61 3.9 44.7 0.8
O A:HOH576 4.0 47.6 1.0
OD1 A:ASP61 4.0 45.0 0.2
CA1 A:OEY415 4.1 46.9 0.8
O A:SER169 4.1 47.7 0.8
O A:HOH605 4.2 52.2 1.0
CG A:GLU333 4.3 48.1 0.8
CB A:ASP170 4.3 43.2 0.8
O A:SER169 4.3 45.6 0.2
OE2 C:GLU354 4.4 53.2 0.2
CG A:GLU333 4.4 45.5 0.2
OE2 C:GLU354 4.4 54.3 0.8
CB A:ASP170 4.4 43.6 0.2
NH2 C:ARG357 4.4 42.9 1.0
CA A:ASP170 4.5 42.9 0.8
O3 A:OEX414 4.6 46.3 0.2
CA A:ASP170 4.6 42.5 0.2
O3 A:OEY415 4.6 46.6 0.8
O D:HOH532 4.7 40.5 1.0
C A:SER169 4.8 45.9 0.8
CG A:ASP61 4.8 44.7 0.8
C A:SER169 4.9 45.1 0.2
N A:ASP170 4.9 42.7 0.8
MN1 A:OEX414 4.9 49.0 0.2
CG A:ASP61 4.9 44.4 0.2
N A:ASP170 5.0 43.7 0.2
OG A:SER169 5.0 48.3 0.2

Manganese binding site 9 out of 16 in 5ws6

Go back to Manganese Binding Sites List in 5ws6
Manganese binding site 9 out of 16 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn412

b:56.3
occ:0.20
 MN1 a:OEX412 0.0 56.3 0.2
MN1 a:OEY413 0.1 56.0 0.8
OE2 a:GLU189 1.8 55.3 0.2
OE2 a:GLU189 1.8 57.1 0.8
O1 a:OEY413 1.8 74.7 0.8
O1 a:OEX412 1.8 74.1 0.2
O3 a:OEY413 1.9 53.6 0.8
O3 a:OEX412 1.9 54.9 0.2
NE2 a:HIS332 2.1 48.1 0.2
NE2 a:HIS332 2.1 49.9 0.8
OD2 a:ASP342 2.1 51.7 0.8
OD2 a:ASP342 2.2 51.1 0.2
O6 a:OEY413 2.3 54.5 0.4
MN2 a:OEY413 2.5 54.9 0.8
MN2 a:OEX412 2.6 55.1 0.2
O5 a:OEX412 2.7 56.3 0.2
O5 a:OEY413 2.8 57.4 0.8
CE1 a:HIS332 2.9 48.9 0.2
CD a:GLU189 2.9 52.4 0.8
CD a:GLU189 2.9 54.5 0.2
CG a:ASP342 3.0 51.3 0.8
CE1 a:HIS332 3.0 48.4 0.8
CG a:ASP342 3.0 51.2 0.2
MN3 a:OEX412 3.1 51.5 0.2
CD2 a:HIS332 3.1 43.4 0.8
CD2 a:HIS332 3.2 45.2 0.2
MN3 a:OEY413 3.2 53.1 0.8
OD1 a:ASP342 3.2 54.7 0.8
OD1 a:ASP342 3.2 52.8 0.2
O2 a:OEY413 3.4 50.9 0.8
CA1 a:OEY413 3.5 58.0 0.8
O2 a:OEX412 3.5 50.5 0.2
OE1 a:GLU189 3.5 58.1 0.8
OE1 a:GLU189 3.5 55.9 0.2
CA1 a:OEX412 3.6 61.2 0.2
NE2 a:HIS337 3.9 46.9 0.2
NE2 a:HIS337 3.9 47.0 0.8
OE1 a:GLU333 3.9 51.1 0.8
OE1 a:GLU333 3.9 51.9 0.2
ND1 a:HIS332 4.1 48.2 0.2
OXT a:ALA344 4.1 51.6 0.8
CG a:GLU189 4.1 51.6 0.2
CG a:GLU189 4.1 50.2 0.8
ND1 a:HIS332 4.1 49.3 0.8
OXT a:ALA344 4.2 51.7 0.2
CG a:HIS332 4.2 46.0 0.2
CG a:HIS332 4.2 45.9 0.8
O a:HOH594 4.2 78.6 1.0
OE1 c:GLU354 4.4 50.3 0.8
OE1 c:GLU354 4.4 50.6 0.2
CB a:ASP342 4.4 49.5 0.8
CB a:ASP342 4.4 49.1 0.2
OE2 c:GLU354 4.5 51.1 0.2
OE2 c:GLU354 4.5 52.2 0.8
O a:ALA344 4.6 50.9 0.8
CE1 a:HIS337 4.6 46.3 0.2
CE1 a:HIS337 4.7 45.2 0.8
CG1 a:VAL185 4.7 46.4 0.2
C a:ALA344 4.7 53.8 0.8
O a:ALA344 4.7 51.7 0.2
CD a:GLU333 4.7 52.1 0.2
CG1 a:VAL185 4.7 46.7 0.8
O a:HOH598 4.7 60.5 0.2
CD a:GLU333 4.7 52.5 0.8
C a:ALA344 4.8 52.9 0.2
O a:HOH598 4.8 60.9 0.8
CD c:GLU354 4.8 51.3 0.2
CD c:GLU354 4.8 50.9 0.8
CD2 a:HIS337 4.9 48.4 0.8
MN4 a:OEX412 4.9 56.1 0.2
CD2 a:HIS337 4.9 47.7 0.2
O4 a:OEX412 4.9 50.0 0.2

Manganese binding site 10 out of 16 in 5ws6

Go back to Manganese Binding Sites List in 5ws6
Manganese binding site 10 out of 16 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn412

b:55.1
occ:0.20
 MN2 a:OEX412 0.0 55.1 0.2
MN2 a:OEY413 0.1 54.9 0.8
O2 a:OEY413 1.8 50.9 0.8
O1 a:OEX412 1.8 74.1 0.2
OXT a:ALA344 1.8 51.6 0.8
O1 a:OEY413 1.8 74.7 0.8
O2 a:OEX412 1.8 50.5 0.2
OXT a:ALA344 1.9 51.7 0.2
O3 a:OEX412 1.9 54.9 0.2
OE1 c:GLU354 2.0 50.3 0.8
O3 a:OEY413 2.0 53.6 0.8
OE1 c:GLU354 2.1 50.6 0.2
OD1 a:ASP342 2.2 52.8 0.2
OD1 a:ASP342 2.2 54.7 0.8
MN1 a:OEX412 2.6 56.3 0.2
MN1 a:OEY413 2.7 56.0 0.8
MN3 a:OEX412 2.7 51.5 0.2
MN3 a:OEY413 2.7 53.1 0.8
C a:ALA344 2.8 53.8 0.8
C a:ALA344 2.9 52.9 0.2
CD c:GLU354 2.9 51.3 0.2
CD c:GLU354 2.9 50.9 0.8
OE2 c:GLU354 3.0 51.1 0.2
CG a:ASP342 3.0 51.3 0.8
CG a:ASP342 3.0 51.2 0.2
OE2 c:GLU354 3.1 52.2 0.8
O a:ALA344 3.2 50.9 0.8
O a:ALA344 3.2 51.7 0.2
OD2 a:ASP342 3.2 51.7 0.8
OD2 a:ASP342 3.2 51.1 0.2
CA1 a:OEY413 3.4 58.0 0.8
CA1 a:OEX412 3.4 61.2 0.2
O5 a:OEX412 3.6 56.3 0.2
O5 a:OEY413 3.6 57.4 0.8
NE2 a:HIS337 3.9 46.9 0.2
NE2 a:HIS337 3.9 47.0 0.8
OE2 a:GLU189 3.9 57.1 0.8
OE2 a:GLU189 4.0 55.3 0.2
O c:HOH697 4.1 52.7 1.0
O6 a:OEY413 4.1 54.5 0.4
CA a:ALA344 4.1 55.0 0.8
CA a:ALA344 4.2 54.6 0.2
O a:HOH594 4.2 78.6 1.0
O4 a:OEX412 4.2 50.0 0.2
N a:ALA344 4.2 56.1 0.8
N a:ALA344 4.3 55.0 0.2
CG c:GLU354 4.3 51.9 0.2
OE1 a:GLU333 4.3 51.9 0.2
CD2 a:HIS337 4.3 47.7 0.2
OE1 a:GLU333 4.3 51.1 0.8
CG c:GLU354 4.3 53.5 0.8
CD2 a:HIS337 4.3 48.4 0.8
NE2 a:HIS332 4.3 48.1 0.2
O4 a:OEY413 4.4 50.3 0.8
NE2 a:HIS332 4.4 49.9 0.8
CB a:ASP342 4.4 49.1 0.2
CB a:ASP342 4.4 49.5 0.8
NH2 c:ARG357 4.6 43.6 1.0
NH1 c:ARG357 4.8 51.2 1.0
C a:ASP342 4.8 51.5 0.8
CD a:GLU189 4.8 52.4 0.8
CD a:GLU189 4.8 54.5 0.2
CB c:GLU354 4.8 52.0 0.8
CA a:ASP342 4.8 45.4 0.8
CA a:ASP342 4.8 48.9 0.2
OD1 a:ASP170 4.8 52.6 0.8
CB c:GLU354 4.8 51.2 0.2
C a:ASP342 4.8 51.7 0.2
OE1 a:GLU189 4.9 55.9 0.2
OE1 a:GLU189 4.9 58.1 0.8
O a:ASP342 4.9 51.1 0.8
OD1 a:ASP170 4.9 51.4 0.2

Reference:

M.Suga, F.Akita, M.Sugahara, M.Kubo, Y.Nakajima, T.Nakane, K.Yamashita, Y.Umena, M.Nakabayashi, T.Yamane, T.Nakano, M.Suzuki, T.Masuda, S.Inoue, T.Kimura, T.Nomura, S.Yonekura, L.J.Yu, T.Sakamoto, T.Motomura, J.H.Chen, Y.Kato, T.Noguchi, K.Tono, Y.Joti, T.Kameshima, T.Hatsui, E.Nango, R.Tanaka, H.Naitow, Y.Matsuura, A.Yamashita, M.Yamamoto, O.Nureki, M.Yabashi, T.Ishikawa, S.Iwata, J.R.Shen. Light-Induced Structural Changes and the Site of O=O Bond Formation in Psii Caught By Xfel. Nature V. 543 131 2017.
ISSN: ESSN 1476-4687
PubMed: 28219079
DOI: 10.1038/NATURE21400
Page generated: Sun Oct 6 03:23:30 2024

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